def _strandMergeUpdate(self, old_strand_low: Strand,
old_strand_high: Strand,
new_strand: Strand):
"""This method sets the isCircular status of the oligo and the oligo's
5' strand.
"""
# check loop status
if old_strand_low.oligo() == old_strand_high.oligo():
self._is_circular = True
self._strand5p = new_strand
return
# leave the _strand5p as is?
# end if
# Now get correct 5p end to oligo
if old_strand_low.isForward():
if old_strand_low.connection5p() is not None:
self._strand5p = old_strand_low.oligo()._strand5p
else:
self._strand5p = new_strand
else:
if old_strand_high.connection5p() is not None:
self._strand5p = old_strand_high.oligo()._strand5p
else:
self._strand5p = new_strand
def __init__(self, strandset: StrandSetT, strand: Strand, solo: bool = True):
super(RemoveStrandCommand, self).__init__("remove strands")
self._strandset = strandset
self._strand = strand
self._solo = solo
self._old_strand5p = strand.connection5p()
self._old_strand3p = strand.connection3p()
self._oligo = olg = strand.oligo()
part = strand.part()
# idxs = strand.idxs()
self.mids = (part.getModID(strand, strand.lowIdx()),
part.getModID(strand, strand.highIdx()))
# only create a new 5p oligo if there is a 3' connection
self._new_oligo5p = olg.shallowCopy() if self._old_strand5p else None
if olg.isCircular() or self._old_strand3p is None:
self._new_oligo3p = olg3p = None
if self._new_oligo5p:
self._new_oligo5p._setLoop(False)
else:
self._new_oligo3p = olg3p = olg.shallowCopy()
olg3p.setStrand5p(self._old_strand3p)
# color_list = styles.STAP_COLORS if strandset.isStaple() else prefs.SCAF_COLORS
color_list = pathstyles.STAP_COLORS
color = random.choice(color_list)
olg3p._setColor(color)
olg3p.refreshLength(emit_signals=True)
def __init__(self,
strandset: StrandSetT,
strand: Strand,
solo: bool = True):
super(RemoveStrandCommand, self).__init__("remove strands")
self._strandset = strandset
self._strand = strand
self._solo = solo
self._old_strand5p = strand.connection5p()
self._old_strand3p = strand.connection3p()
self._oligo = olg = strand.oligo()
part = strand.part()
# idxs = strand.idxs()
self.mids = (part.getModID(strand, strand.lowIdx()),
part.getModID(strand, strand.highIdx()))
# only create a new 5p oligo if there is a 3' connection
self._new_oligo5p = olg.shallowCopy() if self._old_strand5p else None
if olg.isCircular() or self._old_strand3p is None:
self._new_oligo3p = olg3p = None
if self._new_oligo5p:
self._new_oligo5p._setLoop(False)
else:
self._new_oligo3p = olg3p = olg.shallowCopy()
olg3p.setStrand5p(self._old_strand3p)
# color_list = styles.STAP_COLORS if strandset.isStaple() else prefs.SCAF_COLORS
color_list = pathstyles.STAP_COLORS
color = random.choice(color_list)
olg3p._setColor(color)
olg3p.refreshLength(emit_signals=True)
def _strandMergeUpdate(self, old_strand_low: Strand,
old_strand_high: Strand, new_strand: Strand):
"""This method sets the isCircular status of the oligo and the oligo's
5' strand.
"""
# check loop status
if old_strand_low.oligo() == old_strand_high.oligo():
self._is_circular = True
self._strand5p = new_strand
return
# leave the _strand5p as is?
# end if
# Now get correct 5p end to oligo
if old_strand_low.isForward():
if old_strand_low.connection5p() is not None:
self._strand5p = old_strand_low.oligo()._strand5p
else:
self._strand5p = new_strand
else:
if old_strand_high.connection5p() is not None:
self._strand5p = old_strand_high.oligo()._strand5p
else:
self._strand5p = new_strand
def _strandSplitUpdate(self, new_strand5p: Strand, new_strand3p: Strand,
oligo3p: OligoT, old_merged_strand: Strand):
"""If the oligo is a loop, splitting the strand does nothing. If the
oligo isn't a loop, a new oligo must be created and assigned to the
new_strand and everything connected to it downstream.
"""
# if you split it can't be a loop
self._is_circular = False
if old_merged_strand.oligo().isCircular():
self._strand5p = new_strand3p
return
else:
if old_merged_strand.connection5p() is None:
self._strand5p = new_strand5p
else:
self._strand5p = old_merged_strand.oligo()._strand5p
oligo3p._strand5p = new_strand3p
def _strandSplitUpdate(self, new_strand5p: Strand,
new_strand3p: Strand,
oligo3p: OligoT,
old_merged_strand: Strand):
"""If the oligo is a loop, splitting the strand does nothing. If the
oligo isn't a loop, a new oligo must be created and assigned to the
new_strand and everything connected to it downstream.
"""
# if you split it can't be a loop
self._is_circular = False
if old_merged_strand.oligo().isCircular():
self._strand5p = new_strand3p
return
else:
if old_merged_strand.connection5p() is None:
self._strand5p = new_strand5p
else:
self._strand5p = old_merged_strand.oligo()._strand5p
oligo3p._strand5p = new_strand3p
